Peptide



Peptides are short chains of amino acids linked by peptide bonds. By convention, a peptide is not more than 30-50 amino acids in length. Longer chains of amino acids are called polypeptides or proteins. Wikipedia offers a good discussion of peptides, with examples.

Peptides & Backbones
This is the backbone of 1 amino acid. Adding to the backbone with an additional amino acid on each side gives a tripeptide (3 amino acids). No side groups are shown, and most hydrogens are omitted. Now each amino acid has a 1 carbon side group so we have Ala-Ala-Ala (tri-alanine). Adding a carbon chain plus an NH3 on the first amino acid gives Lys-Ala-Ala. Adding  three more carbons to the 3rd amino acid gives isoleucine: Lys-Ala-Ile. The 4th amino acid is threonine with its hydroxyl, giving Lys-Ala-Ile-Thr. Here is the shape of the tetrapeptide (4 AAs). The stick representation has too much detail for larger proteins, so the α-carbons are connected with a line called the backbone trace. Showing only the backbone makes it easier to see the path of the protein chain (its secondary and tertiary structure).

External Resources

 * PepX: a structural database of protein-peptide complexes

Content Attribution
The above scenes in Jmol were adapted from the chapter Peptides and Backbones in a tutorial on Hemoglobin first written by Eric Martz as a RasMol Movie Script released in March, 1996, which was released as a Hemoglobin Tutorial implemented with Chime in September, 1997, and a Hemoglobin Tutorial implemented with Jmol in July 2007.